ZnO has shown great promise for the application in optoelectronic devices. Since the modulation of conductivity is one of the key issues in device performances, we have applied the Monte Carlo method to analyze the mobility of poly-crystalline MgZnO/ZnO heterostructure thin film layer in this paper. The effects of the grain boundary scattering, ionized impurity scattering, as well as phonon scattering are considered. Our study shows that with a design of modulation doping by including the effects of spontaneous and piezoelectric polarization, the grain boundary potential can be suppressed to improve the mobility of the ZnO layer by order(s) of magnitude. Simulation results are also confirmed by our experimental works that polarization effects play an important role to attract carriers and to increase the mobility.